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- PDB-5yl0: The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yl0 | ||||||
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Title | The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) | ||||||
![]() | Capsid protein | ||||||
![]() | VIRAL PROTEIN / viral capsid protein | ||||||
Function / homology | Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit / viral capsid / structural molecule activity / metal ion binding / Capsid protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen / ![]() ![]() ![]() Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of = 3 and = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls = 3 and = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 498.8 KB | Display | |
Data in XML | ![]() | 44.7 KB | Display | |
Data in CIF | ![]() | 68.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6999C ![]() 9576C ![]() 5ykuC ![]() 5ykvC ![]() 5ykxC ![]() 5ykzC ![]() 5yl1C ![]() 6ab5C ![]() 6ab6C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12558.083 Da / Num. of mol.: 4 / Fragment: UNP residues 250-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.075M Magnesium chloride hexahydrate, 0.1M Sodium cacodylate 6.5, 30%(w/v) PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→30 Å / Num. obs: 134587 / % possible obs: 86.9 % / Redundancy: 4.5 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.128 / Rsym value: 0.112 / Net I/σ(I): 38.6 |
Reflection shell | Redundancy: 4.8 % / CC1/2: 0.856 / Rpim(I) all: 0.214 / Rrim(I) all: 0.49 / Rsym value: 0.438 / % possible all: 86.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.942 Å2
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Refinement step | Cycle: 1 / Resolution: 1.22→23.26 Å
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Refine LS restraints |
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